The problem with just about every virtual desktop implementation is just that - they're virtual. This means that beyond the ability to move windows to specific desktops, you're still looking at exactly the same desktop, no matter what virtual desktop number you switched to. A mockup for GNOME Shell is trying to take the virtual out of virtual desktop.

Nice idea, but wouldn't that require a fully metadata-capable filesystem to do correctly? Otherwise, you'd end up with dot files like those OS X generates and wouldn't that just be wonderful.

Extended attributes allow you to add metadata to files and nowadays almost all filesystems support those. Though, I don't know how efficient they are. And it might be better if the filesystem itself had support for easily searching and browsing metadata information, much like f.ex. BeFS.